Vibrio mimicus Lineage Carrying Cholera Toxin and Vibrio Pathogenicity Island, United States and China.

Vibrio mimicus bacteria have caused sporadic cases and outbreaks of cholera-like diarrhea throughout the world, but the association of lineages with such events is unexplored. Genomic analyses revealed V. mimicus lineages carrying the virulence factors cholera toxin and toxin coregulated pilus, one of which has persisted for decades in China and the United States.

Heavy metal resistance in the Yanomami and Tunapuco microbiome.

BACKGROUND: The Amazon Region hosts invaluable and unique biodiversity as well as mineral resources. Consequently, large illegal and artisanal gold mining areas exist in indigenous territories. Mercury has been used in gold mining, and some has been released into the environment and atmosphere, primarily affecting indigenous people such as the Yanomami. In addition, other heavy metals have been associated with gold mining and other metal-dispersing activities in the region. OBJECTIVE: Investigate the gut microbiome of two semi-isolated groups from the Amazon, focusing on metal resistance. METHODS: Metagenomic data from the Yanomami and Tunapuco gut microbiome were assembled into contigs, and their putative proteins were searched against a database of metal resistance proteins. FINDINGS: Proteins associated with mercury resistance were exclusive in the Yanomami, while proteins associated with silver resistance were exclusive in the Tunapuco. Both groups share 77 non-redundant metal resistance (MR) proteins, mostly associated with multi-MR and operons with potential resistance to arsenic, nickel, zinc, copper, copper/silver, and cobalt/nickel. Although both groups harbour operons related to copper resistance, only the Tunapuco group had the pco operon. CONCLUSION: The Yanomami and Tunapuco gut microbiome shows that these people have been exposed directly or indirectly to distinct scenarios concerning heavy metals.

Unveiling the genome of a high-risk pandrug-resistant Klebsiella pneumoniae emerging in the Brazilian Amazon Region, 2022.

BACKGROUND: Pandrug-resistant (PDR) Klebsiella pneumoniae has been reported sporadically in many countries and remains rare in Brazil. OBJECTIVES: This study unravelled the genetic determinants involved with the PDR background of a clinical ST11 K. pneumoniae recovered in the Brazilian Amazon Region, where K. pneumoniae genomic and epidemiological information is scarce. METHODS: Kp196 was submitted to the antimicrobial susceptibility test by the disk-diffusion method and minimum inhibitory concentration (MIC) determination. The whole genome sequencing was obtained and the sequence type was determined by core genome multilocus sequence typing (cgMLST). Its intrinsic and acquired resistome was assessed by Comprehensive Antibiotic Resistance Database (CARD) and comparison with wild-type genes. FINDINGS: The analyses revealed that Kp196 belonged to the pandemic ST11 and presented the PDR phenotype. Its acquired resistome was composed of a huge set of clinically relevant resistance determinants, including bla CTX-M-15 and bla NDM-1, all found in the vicinity of mobile platforms. Considering its intrinsic resistome, the multidrug resistance, especially to colistin, tigecycline and fluoroquinolones, was multifactorial and attributed to modifications (indels, missense mutations, and gene disruption) in several housekeeping genes (arnT/phoQ/mgrB/ramR/acrB/gyrA/parC/ompK35-36-37). The Kp196 intrinsic resistome was also observed in a ST11 environmental strain, although harbouring distinct acquired resistomes. CONCLUSIONS: An accumulation of different resistance mechanisms regarding the intrinsic resistome accounts for a more stable resistome, strongly contributing to the Kp196 PDR phenotype.

Zoonotic Giardia duodenalis assemblage A in northern sloth from Brazilian Amazon.

BACKGROUND: The parasite Giardia duodenalis infects a wide range of vertebrate hosts, including domestic and wild animals as well as humans. Giardia is genotyped into eight assemblages (A-H). Zoonotic assemblages A and B have already been identified in humans and wild and domestic animals (non-human primates and cats) from Brazilian Amazon and in the world. Due to its zoonotic/zooanthroponotic nature, surveillance initiatives and the definition of Giardia assemblages are important in order to characterise the epidemiological scenario and to implement further control measures. OBJECTIVES: Determine assemblages of G. duodenalis in sloths from the Brazilian Amazon Region. METHODS: Faecal parasitological examination of sloths from Amazonas State. Polymerase chain reaction (PCR) targeting the beta giardin (BG), and genes from multilocus sequence typing (MLST) scheme, amplicon sequencing and phylogenetic analysis. FINDINGS: Here, we identified, by microscopy, Giardia in two northern sloths (Bradypus tridactylus). These two samples were submitted to molecular assays and it was revealed that both were infected by G. duodenalis assemblage A. Phylogenetic analysis showed that they belong to assemblage A within sequences from humans and wild and domestic animals. CONCLUSION: Therefore, besides showing, by the first time, the current presence of this parasite in sloths, our findings reveals that this wild animal species would be part of the zoonotic/zooanthroponotic scenario of this parasite in the Brazilian Amazon.

Orange molasses as a new energy ingredient for feedlot lambs in Brazil.

The objectives of this experiment were to evaluate the effects of increasing levels of orange molasses in replacement of flint corn grain in high-concentrate diets on dry matter intake (DMI), average daily gain (ADG), and feed efficiency (FE) of feedlot lambs. Thirty male lambs without defined racial pattern (30.3 ± 5.3 kg of initial BW; mean ± SD) were used in a randomized complete block design with 10 blocks and 3 treatments. The treatments were defined by partial replacement of flint corn by orange molasses in the diet with 90% of concentrate and 10% of Cynodon spp. hay, as follows: 0OM-control diet without orange molasses; 20OM-20% of orange molasses replacing flint corn; and 40OM-40% of orange molasses replacing flint corn (DM basis). The experiment lasted 72 days divided into 3 subperiods, with 1 subperiod of 16 days and 2 subperiods of 28 days. Animals were weighed after a 16-h fast on days 1, 16, 44, and 72 of the experimental periods to determine the ADG and FE. The DMI, ADG, and FE showed an interaction between treatments and experimental periods. The DMI in the first period decreased linearly (P < 0.01); in the third period, there was no effect of treatments (P > 0.05) on DMI. The ADG decreased linearly (P < 0.01) in the first period as the orange molasses increased. Otherwise, in the third period, ADG increased linearly (P = 0.05) as flint corn was replacement by orange molasses. The FE showed an interaction between treatment and period (P = 0.09). The first period had a decreased linear effect; in the third period, there was a trend (P = 0.07) of increased linear effect. There was no difference between the diets regarding the final BW of the lambs. In conclusion, the orange molasses can replace up to 40% of flint corn in diets for feedlot lambs without affecting final BW. However, it is important to consider the adaptation time proved to be very important for better use of orange molasses as a source of energy in diets for lambs.

Processing methods of flint corn and protein supplement in forage-free diets for feedlot lambs.

Diets without forage increase the productivity in less time and favor greater practicality and better quality carcass. The corn grain is mostly used associated with pellets but processing these ingredients can bring benefits. The present study evaluated the effect of diets without forage based on whole or coarse ground corn associated with pelleted or ground protein supplement on performance, eating behavior, carcass characteristics, and ruminal morphology of feedlot lambs. Thirty-five Dorper × Santa Inês lambs were used, with 23.85 ± 3.88 kg of initial body weight and 88 ± 9 days old. The experimental design was in a randomized complete block, defined by body weight and age. The experimental diets were control (CONT), containing 90% of concentrate and 10% of forage (coastcross hay), and 4 diets without forage: WC+P, 70% whole flint corn and 30% pelleted protein supplement; WC+G, 70% whole flint corn and 30% ground protein supplement; GC+P, 70% ground flint corn and 30% pelleted protein supplement; and GC+G, 70% ground flint corn and 30% ground protein supplement. There was an interaction between treatments and experimental periods for DMI in kg/day (P = 0.01) and g/kg of BW0.75 (P < 0.01; Table 3). For the DMI in kg/day, no significant differences were observed between the treatments in any of the experimental periods. However, for DMI expressed in g/kg of BW0.75, the animals fed WC+P had lower DMI than the animals on the CONT (P < 0.01) only in the first period. The ADG, FBW, and FE were not affected by the treatments. Compared to CONT, forage-free diets decreased ingestion time (min/day) and rumination and chewing (min/day and min/g of dry matter). There was no effect of treatments for any of the carcass traits evaluated. The diets did not cause lesions suggestive of ruminitis. Forage-free diets containing whole or ground corn associated with pelleted or ground protein supplement can be used successfully for feedlot lambs; they provide proper performance and carcass characteristics, without harming the animal's health.

Mycolicibacterium fortuitum genomic epidemiology, resistome and virulome.

BACKGROUND: Mycolicibacterium fortuitum is an opportunistic pathogen associated with human and animal infection worldwide. Studies concerning this species are mainly represented by case reports, some of them addressing drug susceptibility with a focus on a specific geographic region, so there is a gap in relation to the global epidemiological scenario. OBJECTIVES: We aimed determine the global epidemiological scenario of M. fortuitum and analyse its traits associated with pathogenicity. METHODS: Based on publicly available genomes of M. fortuitum and a genome from Brazil (this study), we performed a genomic epidemiology analysis and in silico and in vitro characterisation of the resistome and virulome of this species. FINDINGS: Three main clusters were defined, one including isolates from the environment, human and animal infections recovered over nearly a century. An apparent intrinsic resistome comprises mechanisms associated with macrolides, beta-lactams, aminoglycosides and antitubercular drugs such as rifampin. Besides, the virulome presented Type VII secretion systems (T7SS), including ESX-1, ESX-3, ESX-4 and ESX-4-bis, some of which play a role on the virulence of Mycobacteriaceae species. MAIN CONCLUSIONS: Here, M. fortuitum was revealed as a reservoir of an expressive intrinsic resistome, as well as a virulome that may contribute to its success as a global opportunist pathogen.

Giardiasis in urban and rural Amazonas, Brazil is driven by zoonotic and cosmopolitan A and B assemblages.

BACKGROUND: Giardia duodenalis is a protozoan parasite that infects humans and other mammals and causes giardiasis worldwide. Giardia is genotyped into eight assemblages (A-H), with assemblages A and B considered zoonotic. OBJECTIVES: The aim of this study was to determine the assemblages of G. duodenalis from individuals living in rural and urban areas of the Amazonas State. METHODS: 103 human faecal specimens microscopically positive for the presence of Giardia obtained from four municipalities in Amazonas and four animal faecal specimens were genotyped based on the sequences of two genes, triosephosphate isomerase (TPI) and ß-giardin (BG). FINDINGS: In humans, assemblage A was the most represented with the identification of sub-assemblages AI, AII and AIII based on BG and sub-assemblages AI and AII based on TPI. Similarly, there is a diversity of sub-assemblage B considering BG (B and BIII) and TPI (B, BIII and BIV). In addition, we characterised homogeneous and heterogeneous genotypes comprising assemblages/sub-assemblages A and B in individuals from urban and rural areas. Here, for the first time, it was genotyped Giardia that infects animals from the Brazilian Amazon region. We identified sub-assemblage AI in one Ateles paniscus and two Felis catus and sub-assemblage BIV in one Lagothrix cana. MAIN CONCLUSIONS: Therefore, humans and animals from the urban and rural Amazon share Giardia genotypes belonging to assemblages A and B, which are found in cosmopolitan regions around the world.

Performance, nutritional behavior, and carcass characteristics of feedlot lambs fed diets with non-forage fiber source or sodium bicarbonate.

The study was carried out to evaluate the effect of sodium bicarbonate (SB) supplementation in diets and compare its chemical effect with the fiber effect of soybean hulls on performance, nutritional behavior, and carcass characteristics of feedlot lambs. Twenty-eight ram lambs (Dorper × Santa Inês), with an initial body weight of 30.2 ± 4.5 kg and 94 ± 8.4 days old, were used. They were assigned to a randomized complete block design, defined by initial age and body weight. Experimental diets were positive control, diet containing soybean hulls in 400 g/kg dry matter (DM) (CONT), and three diets based on ground flint corn containing 10 (10SB), 20 (20SB), or 30 (30SB) g/kg DM of SB. Among the SB levels, the buffer supplementation quadratically increased dry matter intake, average daily gain, feed efficiency, as well as increased final and slaughter body weight, which led to higher hot and cold carcass weights, loin muscle area, leg compacity index, and weight of neck, shoulder, rib, and leg cuts, with higher values for the 20SB. Feeding SB linearly decreased the area and height of the papillae. None of the animals presented liver abscess; however, two animals from 30SB and one from CONT had F-rumen lesions. The use of SB provided a similar animal performance when compared to the treatment containing soybean hulls. This shows that the chemical effect of the buffer was efficient and provided greater safety for this type of diet without causing damages to the rumen health. Among the SB levels, the best results were observed in the 20 g/kg level (20SB), which shows that the buffer can be used as a strategy for diets with high inclusion of corn and no fiber source.

Polymorphisms in HTLV-1 Tax-responsive elements in HTLV-1-associated myelopathy/tropical spastic paraparesis patients are associated with reduced proviral load but not with disease progression.

Human T-lymphotropic virus type 1 (HTLV-1) provirus expression is mainly directed by Tax-responsive elements (TRE) within the long terminal repeats (LTR). Mutations in TRE can reduce provirus expression and since a high proviral load (PVL) is a risk factor for the development of HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP), we evaluated polymorphisms in the 5' LTR and the association with PVL and disease progression. HTLV-1 LTR and tax sequences derived from asymptomatic carriers (AC) and HAM/TSP patients followed in a longitudinal study were analysed according to PVL and clinical severity. Individuals infected with HTLV-1 presenting the canonical TRE, considering strain ATK-1 as the consensus, displayed sustained higher PVL. By contrast, an LTR A125G mutation in TRE was associated with slightly reduced PVL only in HAM/TSP patients, although it did not influence the speed of disease progression. Moreover, this polymorphism was frequent in Latin American strains of the HTLV-1 Cosmopolitan Transcontinental subtype. Therefore, polymorphisms in the 5' TRE of HTLV-1 may represent one of the factors influencing PVL in HAM/TSP patients, especially in the Latin American population. Indeed, higher PVL in the peripheral blood has been associated with an increased inflammatory activity in the spinal cord and to a poorer prognosis in HAM/TSP. However, this event was not associated with TRE polymorphisms.

Deep Sequencing Reveals Occult Mansonellosis Coinfections in Residents From the Brazilian Amazon Village of São Gabriel da Cachoeira.

Mansonella ozzardi and Mansonella perstans infections both cause mansonellosis but are usually treated differently. Using a real-time polymerase chain reaction assay and deep sequencing, we reveal the presence of mansonellosis coinfections that were undetectable by standard diagnostic methods. Our results confirm mansonellosis coinfections and have important implications for the disease's treatment and diagnosis.

The rare lncRNA GOLLD is widespread and structurally conserved among Mycobacterium tRNA arrays.

Noncoding RNA (ncRNA) genes produce transcripts involved in a wide range of functions, including catalytic and regulatory functions. Besides, some transcripts have highly complex structures that may impact their activities. Among the largest bacterial ncRNAs, there is the rare GOLLD RNA, which is associated with tRNA genes and supposed to be chromosome- and phage-encoded in specialized groups of bacteria, including those from Lactobacillales and Actinomycetales orders. The only GOLLD structure was inferred from a variety of sequences, including many marine metagenomes. To explore GOLLD RNA in bacterial genomes, we mined the GOLLD gene in thousands of Mycobacterium and virus genomes using Infernal software. We identified this gene in 350 mycobacteria, including megaplasmids, and 39 bacteriophages, mainly in the genomic context of tRNA arrays. Mycobacterium GOLLD genes presented a high diversity and were distributed in three phylogenetic groups: (i) Mycobacterium exclusive; (ii) Mycobacterium and mycobacteriophages; and (iii) mycobacteriophage exclusive. We also determined the GOLLD secondary structure of each group using R2 R software based on GOLLD alignments generated by Infernal software. All GOLLD groups displayed a 3' half conserved structure, including utter E-loops pseudoknots substructures, also shared by non-Mycobacterium GOLLD while the 5' half motif was different among the groups. Here, we showed that the lncRNA GOLLD is widespread in Mycobacterium within tRNA arrays and corroborated the previously predicted GOLLD secondary structure.

Pyomelanin biosynthetic pathway in pigment-producer strains from the pandemic Acinetobacter baumannii IC-5.

BACKGROUND: Acinetobacter baumannii outbreaks have been associated with pandemic International Clones (ICs), but the virulence factors involved with their pathogenicity are sparsely understood. Pigment production has been linked with bacterial pathogenicity, however, this phenotype is rarely observed in A. baumannii. OBJECTIVES: This study aimed to characterise the reddish-brown pigment produced by A. baumannii strains, and to determine its biosynthetic pathway by genomic approaches. METHODS: Pigment characterisation and antimicrobial susceptibility were conducted by phenotypic tests. The clonal relationship was obtained by pulsed field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). The genome of an A. baumannii was obtained for characterisation of genes involved with pigment production. FINDINGS: The pyomelanin was the pigment produced by A. baumannii. Strains were extensively drug resistant and belonged to the IC-5/ST79. The pyomelanin biosynthetic pathway was determined and presented a particular architecture concerning the peripheral (tyrB, phhB and hpd) and central (hmgB, hmgC and hmgR) metabolic pathway genes. The identification of a distant HmgA homologue, probably without dioxygenase activity, could explain pyomelanin production. Virulence determinants involved with adherence (csuA/BABCDE and a T5bSS-carrying genomic island), and iron uptake (basABCDEFGHIJ, bauABCDEF and barAB) were characterised. MAIN CONCLUSION: There is a biosynthetic pathway compatible with the pyomelanin production observed in persistent A. baumannii IC-5 strains.

Mycobacterium genus and tRNA arrays.

The presence of tRNA array, a region with high tRNA gene number and density, has been demonstrated in Mycobacterium genus. However, a recent phylogenomic study revealed the existence of five distinct monophyletic groups (genera) within this genus. Considering this new scenario, and based on in-silico analyses, we have identified and characterised the abundance and diversity of tRNA array units within Mycobacterium, Mycolicibacterium gen. nov., Mycolicibacillus gen. nov., and Mycobacteroides gen. nov. The occurrence and prevalence of tRNA arrays among the genera belonging to Actinobacteria indicate their possible role in the organismal fitness.

Exploring tRNA gene cluster in archaea.

BACKGROUND: Shared traits between prokaryotes and eukaryotes are helpful in the understanding of the tree of life evolution. In bacteria and eukaryotes, it has been shown a particular organisation of tRNA genes as clusters, but this trait has not been explored in the archaea domain. OBJECTIVE: Explore the occurrence of tRNA gene clusters in archaea. METHODS: In-silico analyses of complete and draft archaeal genomes based on tRNA gene isotype and synteny, tRNA gene cluster content and mobilome elements. FINDINGS: We demonstrated the prevalence of tRNA gene clusters in archaea. tRNA gene clusters, composed of archaeal-type tRNAs, were identified in two Archaea class, Halobacteria and Methanobacteria from Euryarchaeota supergroup. Genomic analyses also revealed evidence of the association between tRNA gene clusters to mobile genetic elements and intra-domain horizontal gene transfer. MAIN CONCLUSIONS: tRNA gene cluster occurs in the three domains of life, suggesting a role of this type of tRNA gene organisation in the biology of the living organisms.

Acinetobacter baumannii infections in Amazon Region driven by extensively drug resistant international clones, 2016-2018.

BACKGROUND: Acinetobacter baumannii is a leading cause of nosocomial infections. This species is characterised by the presence of pandemic lineages (International Clones) that present a broad antimicrobial resistance profile. OBJECTIVE: To perform the molecular epidemiology of carbapenem-resistant A. baumannii from a clinical setting in the Amazon Basin, and to characterise their antimicrobial resistance determinants. METHODS: The genetic relationship of carbapenem-resistant A. baumannii were assessed by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Class A, B and D ß-lactamase genes were screened by polymerase chain reaction (PCR) and sequencing. The antimicrobial susceptibility profile was obtained by Disc-diffusion method and minimum inhibitory concentration (MIC) determination. FINDINGS: All carbapenem-resistant A. baumannii strains belonged to three international clones, IC-1, IC-5 and IC-6, the latter recently reported by the first time in Brazil. The major determinant of carbapenem resistance in IC-1 and IC-5 strains was bla OXA-23, associated with ISAba1 and ISAba3, respectively, while IC-6 harboured the bla OXA-72. CONCLUSIONS: The A. baumannii epidemiology in Brazilian Amazon Region was unknown. It was demonstrated that A. baumannii XDR international clones were responsible for nosocomial infections in Boa Vista during 2016-2018, revealing that the epidemiological scenario of A. baumannii infections in Amazon Region resembles those from the cosmopolitan regions worldwide.

Genomic and structural features of the yellow fever virus from the 2016-2017 Brazilian outbreak.

Southeastern Brazil has been suffering a rapid expansion of a severe sylvatic yellow fever virus (YFV) outbreak since late 2016, which has reached one of the most populated zones in Brazil and South America, heretofore a yellow fever-free zone for more than 70 years. In the current study, we describe the complete genome of 12 YFV samples from mosquitoes, humans and non-human primates from the Brazilian 2017 epidemic. All of the YFV sequences belong to the modern lineage (sub-lineage 1E) of South American genotype I, having been circulating for several months prior to the December 2016 detection. Our data confirm that viral strains associated with the most severe YF epidemic in South America in the last 70 years display unique amino acid substitutions that are mainly located in highly conserved positions in non-structural proteins. Our data also corroborate that YFV has spread southward into Rio de Janeiro state following two main sylvatic dispersion routes that converged at the border of the great metropolitan area comprising nearly 12 million unvaccinated inhabitants. Our original results can help public health authorities to guide the surveillance, prophylaxis and control measures required to face such a severe epidemiological problem. Finally, it will also inspire other workers to further investigate the epidemiological and biological significance of the amino acid polymorphisms detected in the Brazilian 2017 YFV strains.

HTLV-1 and -2 in a first-time blood donor population in Northeastern Brazil: Prevalence, molecular characterization, and evidence of intrafamilial transmission.

Independent epidemiology for respective human T-cell lymphotropic virus (HTLV) types 1 and 2 is little known in blood donors in Brazil, where screening for HTLV-1/2 is mandatory at blood banks, but no testing to confirm/differentiate these viruses. Therefore, this study aims to assess the prevalence of HTLV-1 and -2 in a first-time blood donor population in Northeastern Brazil and to carry out molecular characterization of respective isolates. A cross-sectional study was conducted at the State Blood Bank in Piauí. Samples were screened for anti-HTLV-1/2 by enzyme immunoassay, and reactive samples were confirmed using a line immunoassay and polymerase chain reaction (PCR). Of 37 306 blood donors, 47 were anti-HTLV-1/2 reactive by enzyme immunoassay. After confirmed by line immunoassay, 22 were positive for HTLV-1 (0.59 per 1000; 95% CI: 0.38-0.87), 14 were positive for HTLV-2 (0.37 per 1000; 95% CI: 0.21-0.61), 1 was indeterminate, and the remaining donors were negative. The HTLV-1 infection was also confirmed by PCR in all anti-HTLV-1-positive samples, and sequencing classified these isolates as belonging to the Transcontinental (A) subgroup of the Cosmopolitan (1a) subtype. Of 14 anti-HTLV-2-positive samples, 11 were also PCR positive, which belonged to subtype a (HTLV-2a/c). In addition, 38 family members of 5 HTLV-1- and 3 HTLV-2-infected donors were analyzed. Familial transmission of HTLV-1 and -2 was evidenced in 3 families. In conclusion, in Northeastern Brazil, where HTLV-1 and -2 are endemic, counseling blood donor candidates and their families might play a key role in limiting the spread of these viruses.